sisl.io.openmx.omxSileOpenMX

class sisl.io.openmx.omxSileOpenMX[source]

Bases: SileOpenMX

OpenMX-input file

By supplying base you can reference files in other directories. By default the base is the directory given in the file name.

Parameters:

filename (str) – input file
mode (str, optional) – opening mode, default to read-only
base (str, optional) – base-directory to read output files from.

Examples

>>> omx = omxSileOpenMX("tmp/input.dat") # reads output files in 'tmp/' folder
>>> omx = omxSileOpenMX("tmp/input.dat", base=".") # reads output files in './' folder

When using this file in conjunction with the sgeom script while your input data-files are named input.dat, please do this:

sgeom input.dat{omx} output.xyz

which forces the use of the omx file.

Plotting

`plot`	Plotting functions for the `omxSileOpenMX` class.
`plot.geometry`([output, ...])	Calls `read_geometry` and creates a `GeometryPlot` from its output.

Methods

`base_directory`([relative_to])	Retrieve the base directory of the file, relative to the path relative_to
`close`()
`dir_file`([filename, filename_base])	File of the current Sile
`get`(key[, default])	Retrieve keyword from the file
`read`(args, *kwargs)	Generic read method which should be overloaded in child-classes
`read_basis`(args, *kwargs)	Reads basis
`read_geometry`([output])	Returns Geometry object
`read_lattice`([output])	Reads lattice
`type`(label)	Return the type of the fdf-keyword
`write`(args, *kwargs)	Generic write method which should be overloaded in child-classes

Attributes

`base_file`	File of the current Sile
`file`	Return the current file name (without the directory prefix)

base_directory(relative_to='.'): Retrieve the base directory of the file, relative to the path relative_to

close()

dir_file(filename=None, filename_base=''): File of the current Sile

get(key, default=None)[source]

Retrieve keyword from the file

Parameters:

key (str) – the key to search for
default (optional) – if the key is not found, this will be the returned value (default to None)

Returns:

value – a real value a float (or if the default is of float), for an integer, an int is returned.

Return type:

the value of the key. If the key is a block, a `list is returned`, for

plot.geometry(output=False, *args, data_kwargs={}, axes=['x', 'y', 'z'], atoms=None, atoms_style=[], atoms_scale=1.0, atoms_colorscale=None, drawing_mode=None, bind_bonds_to_ats=True, points_per_bond=20, bonds_style={}, bonds_scale=1.0, bonds_colorscale=None, show_atoms=True, show_bonds=True, show_cell='box', cell_style={}, nsc=(1, 1, 1), atoms_ndim_scale=(16, 16, 1), bonds_ndim_scale=(1, 1, 10), dataaxis_1d=None, arrows=(), backend='plotly')

Calls read_geometry and creates a GeometryPlot from its output.

Parameters:

output (bool) – whether to read geometry from output files (default to read from the input file).
order ({'dat', 'omx'}) – the order of which to try and read the geometry. If order is present output is disregarded.
axes (Axes) – The axes to project the geometry to.
atoms (AtomsIndex) – The atoms to plot. If None, all atoms are plotted.
atoms_style (Sequence[AtomsStyleSpec]) – List of style specifications for the atoms. See the showcase notebooks for examples.
atoms_scale (float) – Scaling factor for the size of all atoms.
atoms_colorscale (Optional[Colorscale]) – Colorscale to use for the atoms in case the color attribute is an array of values. If None, the default colorscale is used for each backend.
drawing_mode (Literal['scatter', 'balls', None]) – The method used to draw the atoms.
bind_bonds_to_ats (bool) – Whether to display only bonds between atoms that are being displayed.
points_per_bond (int) – When the points are drawn using points instead of lines (e.g. in some frameworks to draw multicolor bonds), the number of points used per bond.
bonds_style (StyleSpec) – Style specification for the bonds. See the showcase notebooks for examples.
bonds_scale (float) – Scaling factor for the width of all bonds.
bonds_colorscale (Optional[Colorscale]) – Colorscale to use for the bonds in case the color attribute is an array of values. If None, the default colorscale is used for each backend.
show_atoms (bool) – Whether to display the atoms.
show_bonds (bool) – Whether to display the bonds.
show_cell (Literal['box', 'axes', False]) – Mode to display the cell. If False, the cell is not displayed.
cell_style (StyleSpec) – Style specification for the cell. See the showcase notebooks for examples.
nsc (tuple[int, int, int]) – Number of unit cells to display in each direction.
atoms_ndim_scale (tuple[float, float, float]) – Scaling factor for the size of the atoms for different dimensionalities (1D, 2D, 3D).
bonds_ndim_scale (tuple[float, float, float]) – Scaling factor for the width of the bonds for different dimensionalities (1D, 2D, 3D).
dataaxis_1d (Optional[Union[np.ndarray, Callable]]) – Only meaningful for 1D plots. The data to plot on the Y axis.
arrows (Sequence[AtomArrowSpec]) – List of arrow specifications to display. See the showcase notebooks for examples.
backend – The backend to use to generate the figure.

Return type:

GeometryPlot